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Added js file and demo
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function VQI_GenomeBrowser(id){ | ||
this.div_id = id; | ||
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this.width = 1000; | ||
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this.height = 100; | ||
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this.margin = 50; | ||
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this.genomeData = []; | ||
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this.chromosomes = []; | ||
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$("#" + id).append("<div style='border : 1px solid; display : inline-block'>CPG:<input type='file' id='cpg'/>Shore:<input type='file' id='shore'/>Shelve:<input type='file' id='shelve'/><input id='submit' type='submit' /></div>"); | ||
d3.select("#" + id + " #submit").on("click", this.submitFile.bind(this)); | ||
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d3.select("#" + id).append("div").text("Chromosome: ") | ||
this.select = d3.select("#" + id) | ||
.append("div") | ||
.append("select") | ||
.on("change", function(d) { | ||
self.graph(self.select.property("value")); | ||
}); | ||
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d3.select("#" + id).append("div").text("Start: ") | ||
this.minNumber = d3.select("#" + id) | ||
.append("input") | ||
.attr("type","number") | ||
.property("value",0); | ||
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d3.select("#" + id).append("div").text("End: ") | ||
this.maxNumber = d3.select("#" + id) | ||
.append("input") | ||
.attr("type","number") | ||
.property("value",0); | ||
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var self = this; | ||
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this.graphButton = d3.select("#" + id) | ||
.append("input") | ||
.attr("type","button") | ||
.attr("value","Graph") | ||
.on("click", function(){ | ||
self.graph(self.select.property("value"),self.minNumber.property("value"),self.maxNumber.property("value")) | ||
}); | ||
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this.svg = d3.select("#" + id) | ||
.append("svg") | ||
.attr("width", this.width + 2 * this.margin) | ||
.attr("height", this.height + 2 * this.margin); | ||
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//set up scales and axis | ||
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this.xScale = d3.scale.linear(); | ||
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this.xAxis = d3.svg.axis() | ||
.scale(this.xScale) | ||
.orient("bottom") | ||
.ticks(10); | ||
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this.xAxisSelection = this.svg.append("g") | ||
.call(this.xAxis) | ||
.attr("class", "axis") | ||
.attr("transform", "translate(0,"+ (this.height + this.margin) + ")"); | ||
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this.zoom = d3.behavior.zoom(); | ||
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//set up tool tips | ||
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this.tip = d3.tip() | ||
.attr('class', 'd3-tip') | ||
.offset([-20, 0]) | ||
.html(function(d) { | ||
return "<span style='color:white; font-size:10pt; display:block; text-align:center'>" + d.chromosome + " " + d.type + "</span>" | ||
+ "<span style='color:white; font-size:10pt; display:block'>(" + d.start + " - " + d.end + ")"+ "</span>"; | ||
}); | ||
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this.svg.call(this.tip); | ||
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d3.selectAll(".d3-tip").style({ | ||
"line-height": "1", | ||
"font-weight": "bold", | ||
"padding": "12px", | ||
"background": "rgba(0, 0, 0, 0.8)", | ||
"color": "#fff", | ||
"border-radius": "2px" | ||
}); | ||
} | ||
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VQI_GenomeBrowser.prototype = new VQI_Publisher(); | ||
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VQI_GenomeBrowser.prototype.zoomed = function() { | ||
var self = this; | ||
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self.xAxisSelection.call(self.xAxis); | ||
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self.svg.selectAll("rect") | ||
.attr("width", function (d) {return self.xScale(d.end) - self.xScale(d.start)}) | ||
.attr("x", function(d) {return self.xScale(d.start)}) | ||
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self.minNumber.property("value", self.xScale.domain()[0]); | ||
self.maxNumber.property("value", self.xScale.domain()[1]); | ||
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d3.selectAll(".axis path, .axis line").style({ | ||
"fill": "none", | ||
"stroke": "black", | ||
"shape-rendering": "crispEdges"}); | ||
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d3.selectAll(".axis text").style({ | ||
"font-family": "sans-serif", | ||
"font-size": "11px"}); | ||
} | ||
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VQI_GenomeBrowser.prototype.graph = function(chromosome , min , max){ | ||
//Graphs the current chromosome. If min and max are specified, graph only in that range. | ||
//Otherwise, graphs the whole chromosome | ||
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var self = this; | ||
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var currentData; | ||
var xMax = 0; | ||
var xMin = 0; | ||
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//Populates drop down list with different chromosomes | ||
self.select.selectAll("option") | ||
.data(self.chromosomes) | ||
.enter() | ||
.append("option") | ||
.attr("value", function (d) { return d; }) | ||
.text(function (d) { return d; }) | ||
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//Gets relevant data and calculates min/max if needed | ||
if(min == null || max == null) | ||
{ | ||
currentData = self.genomeData.filter(function(d) {return d.chromosome == chromosome}); | ||
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xMax = d3.max(currentData, function(d) {return d.end}); | ||
xMin = d3.min(currentData, function(d) {return d.start}); | ||
self.minNumber.property("value", xMin); | ||
self.maxNumber.property("value", xMax); | ||
} | ||
else | ||
{ | ||
currentData = self.genomeData.filter(function(d) {return d.chromosome == chromosome && d.start >= min && d.end <= max}); | ||
xMax = Number(max); | ||
xMin = Number(min); | ||
} | ||
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self.xScale.domain([xMin - (xMax - xMin) * 1/10, xMax + (xMax - xMin) * 1/10]) | ||
.range([self.margin, self.width + self.margin]); | ||
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self.xAxisSelection.call(self.xAxis); | ||
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self.zoom.x(self.xScale) | ||
.on("zoom", self.zoomed.bind(self)); | ||
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self.svg.call(self.zoom); | ||
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d3.selectAll(".axis path, .axis line").style({ | ||
"fill": "none", | ||
"stroke": "black", | ||
"shape-rendering": "crispEdges"}); | ||
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d3.selectAll(".axis text").style({ | ||
"font-family": "sans-serif", | ||
"font-size": "11px"}); | ||
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//Just a line | ||
self.svg.append("line") | ||
.attr("x1",self.margin) | ||
.attr("y1",self.height/2 + self.margin + 20) | ||
.attr("x2",self.width+self.margin) | ||
.attr("y2",self.height/2 + self.margin + 20) | ||
.style("stroke", "blue"); | ||
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self.svg.selectAll("rect") | ||
.data(currentData) | ||
.exit() | ||
.remove(); | ||
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self.svg.selectAll("rect") | ||
.data(currentData) | ||
.enter() | ||
.append("rect"); | ||
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self.svg.selectAll("rect") | ||
.style("fill-opacity", ".4") | ||
.style("stroke", function (d) { return d.type == "cpg" ? "red" : d.type == "shore" ? "green" : "yellow"}) | ||
.style("fill", function (d) { return d.type == "cpg" ? "red" : d.type == "shore" ? "green" : "yellow"}) | ||
.attr("height", function (d) { return d.type == "cpg" ? 40 : d.type == "shore" ? 20 : 15}) | ||
.attr("width", function (d) {return self.xScale(d.end) - self.xScale(d.start)}) | ||
.attr("x", function(d) {return self.xScale(d.start)}) | ||
.attr("y", function (d) { var offset = d.type == "cpg" ? 0 : d.type == "shore" ? 10 : 12.5; | ||
return self.height/2 + self.margin + offset}) | ||
.on('mouseover', self.tip.show) | ||
.on('mouseout', self.tip.hide); | ||
} | ||
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VQI_GenomeBrowser.prototype.setData = function(data){ | ||
this.genomeData = data; | ||
this.graph(); | ||
} | ||
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VQI_GenomeBrowser.prototype.getData = function(){ | ||
return this.genomeData; | ||
} | ||
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VQI_GenomeBrowser.prototype.submitFile = function(){ | ||
var self = this; | ||
self.genomeData = []; | ||
self.chromosomes = []; | ||
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//Will read the 3 files and place all data into genomeData | ||
//as objects with attributes 'chromosome', 'start', 'end', 'type' | ||
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$.get($("#" + self.div_id + " #cpg").val().split('\\').pop(), function(data){ | ||
var cpgData = data.trim().split("\n"); | ||
$.each(cpgData , function(index , value){ | ||
cpgData[index] = cpgData[index].trim().split("\t").map(function(item) { | ||
return isNaN(Number(item)) ? item : Number(item); | ||
}); | ||
}); | ||
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//get all unique chromosomes | ||
var currentChromosome = ""; | ||
$.each(cpgData , function(index , value){ | ||
if(value[0] != currentChromosome) | ||
{ | ||
self.chromosomes.push(value[0]); | ||
currentChromosome = value[0]; | ||
} | ||
}); | ||
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cpgData = cpgData.map(function(data){ | ||
return {"chromosome" : data[0], "start" : data[1], "end" : data[2], "type" : "cpg"} | ||
}); | ||
self.genomeData = self.genomeData.concat(cpgData); | ||
}); | ||
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$.get($("#" + self.div_id + " #shore").val().split('\\').pop(), function(data){ | ||
var tempShoreData = data.trim().split("\n"); | ||
$.each(tempShoreData , function(index , value){ | ||
tempShoreData[index] = tempShoreData[index].trim().split("\t").map(function(item) { | ||
return isNaN(Number(item)) ? item : Number(item); | ||
}); | ||
}); | ||
var shoreData = []; | ||
$.each(tempShoreData , function(index , value){ | ||
shoreData.push({"chromosome" : value[0], "start" : value[1], "end" : value[2], "type" : "shore"}); | ||
shoreData.push({"chromosome" : value[0], "start" : value[3], "end" : value[4], "type" : "shore"}); | ||
}); | ||
self.genomeData = self.genomeData.concat(shoreData); | ||
}); | ||
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$.get($("#" + self.div_id + " #shelve").val().split('\\').pop(), function(data){ | ||
var tempShelveData = data.trim().split("\n"); | ||
$.each(tempShelveData , function(index , value){ | ||
tempShelveData[index] = tempShelveData[index].trim().split("\t").map(function(item) { | ||
return isNaN(Number(item)) ? item : Number(item); | ||
}); | ||
}); | ||
var shelveData = []; | ||
$.each(tempShelveData , function(index , value){ | ||
shelveData.push({"chromosome" : value[0], "start" : value[1], "end" : value[2], "type" : "shelve"}); | ||
shelveData.push({"chromosome" : value[0], "start" : value[3], "end" : value[4], "type" : "shelve"}); | ||
}); | ||
self.genomeData = self.genomeData.concat(shelveData); | ||
self.graph(self.chromosomes[0]); | ||
}); | ||
} |
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<head></head> | ||
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<body> | ||
<div id="test"> | ||
</div> | ||
<div id="test2"> | ||
</div> | ||
</body> | ||
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<script src="http://d3js.org/d3.v3.min.js" charset="utf-8"></script> | ||
<script type="text/javascript" src="http://code.jquery.com/jquery-1.10.2.min.js"></script> | ||
<script src="http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script> | ||
<script src="VQI_Publisher.js"></script> | ||
<script src="VQI_GenomeBrowser.js"></script> | ||
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<script type="text/javascript"> | ||
var test = new VQI_GenomeBrowser("test"); | ||
</script> | ||
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